Loss-of-Function Mutation in the Dioxygenase-Encoding FTO Gene Causes Severe Growth Retardation and Multiple Malformations Sarah Boissel, Orit Reish, Karine Proulx, Hiroko Kawagoe-Takaki, Barbara Sedgwick, Giles Yeo, David Meyre, Christelle Golzio, Florence Molinari, Noman Kadhom, et al. To cite this version: Sarah Boissel, Orit Reish, Karine Proulx, Hiroko Kawagoe-Takaki, Barbara Sedgwick, et al.. Loss-of- Function Mutation in the Dioxygenase-Encoding FTO Gene Causes Severe Growth Retardation and Multiple Malformations. American Journal of Human Genetics, Elsevier (Cell Press), 2009, 85 (1), pp.106-111. 10.1016/j.ajhg.2009.06.002. hal-02044723 HAL Id: hal-02044723 https://hal.archives-ouvertes.fr/hal-02044723 Submitted on 21 Feb 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. REPORT Loss-of-Function Mutation in the Dioxygenase-Encoding FTO Gene Causes Severe Growth Retardation and Multiple Malformations Sarah Boissel,1,7 Orit Reish,2,7 Karine Proulx,3,7 Hiroko Kawagoe-Takaki,4 Barbara Sedgwick,4 Giles S.H. Yeo,3 David Meyre,5 Christelle Golzio,1 Florence Molinari,1 Noman Kadhom,1 Heather C. Etchevers,1 Vladimir Saudek,3 I. Sadaf Farooqi,3 Philippe Froguel,5,6 Tomas Lindahl,4 Stephen O’Rahilly,3 Arnold Munnich,1 and Laurence Colleaux1,* FTO is a nuclear protein belonging to the AlkB-related non-haem iron- and 2-oxoglutarate-dependent dioxygenase family. Although polymorphisms within the first intron of the FTO gene have been associated with obesity, the physiological role of FTO remains unknown. Here we show that a R316Q mutation, inactivating FTO enzymatic activity, is responsible for an autosomal-recessive lethal syndrome. Cultured skin fibroblasts from affected subjects showed impaired proliferation and accelerated senescence. These findings indicate that FTO is essential for normal development of the central nervous and cardiovascular systems in human and establish that a mutation in a human member of the AlkB-related dioxygenase family results in a severe polymalformation syndrome. Fto was originally identified in mice as one of the genes en- by oxidative demethylation.10–14 Fto-deficient mice have coded by the 1.6 Mb deletion causing the fused toes (Ft) been recently described.15 Homozygous mutant mice are mutant, an autosomal-dominant mouse mutation gener- viable but postnatal death occurs frequently and loss of ated by a transgene integration into region D of mouse Fto leads to postnatal growth retardation, significant Chr 8.1 In addition to Fto, the deleted segment also reduction in adipose tissue, and lean body mass. contains three members of the Iroquois gene family (Irx3, We ascertained a large Palestinian Arab consanguineous Irx5, and Irx6, also known as the IrxB complex) as well as multiplex family in which nine affected individuals pre- the Fts/Aktip and Ftm/Rpgrip1l genes. Mice heterozygous sented with a previously unreported polymalformation for the Ft mutation are characterized by partial syndactyly syndrome (Figure 1A). The study was approved by the of forelimbs and thymic hyperplasia.1 Ft/Ft embryos die in supreme Israeli Helsinki Review Board (33/07-08) and midgestation and present many abnormalities including informed consent was obtained from all family members. limb polydactyly and distal truncations, major brain and All affected individuals had postnatal growth retardation, heart defects, delay or absence of neural tube closure, microcephaly, severe psychomotor delay, functional brain and facial structure hypoplasia.2,3 deficits, and characteristic facial dysmorphism. In some Interestingly, a human genome-wide search for type 2 patients, structural brain malformations, cardiac defects, diabetes susceptibility genes identified the strong associa- genital anomalies, and cleft palate were also observed tion of a series of single nucleotide polymorphisms (Table 1). Early lethality resulting from intercurrent infec- (SNPs), in tight linkage disequilibrium with rs9939609 tion or unidentified cause occurred at 1–30 months of age. and located in the first intron of the FTO gene (MIM Extensive biochemical, metabolic, and genetic analyses 610966), with higher body mass index (BMI) and obesity failed to diagnose any previously known inherited disor- risk in European cohorts.4,5 This association was replicated ders. Because the pedigree suggested an autosomal-reces- in various European cohorts and several studies have been sive mode of inheritance, we performed a genome-wide performed trying to identify association between the autozygosity screen with the Perkin Elmer Biosystems obesity risk allele and energy intake/expenditure or eating linkage mapping set (version 1) and identified a unique behavior trait.6–8 However, how FTO variants modulate region of shared homozygosity on chromosome 16q12 components of the energy balance remains elusive so far. (Figure S1 available online). Further genotype and haplo- FTO has been recognized as a member of the AlkB-related type analyses reduced the critical region to a 6.5 Mb interval family of non-haem iron- and 2-oxoglutarate-dependent between loci D16S411 and D16S3140 (maximum LOD dioxygenases.9 These non-heme iron enzymes, which score Zmax ¼ 4.16 at q ¼ 0 at the D16S3136 locus). No other require Fe2þ as a cofactor and 2-oxoglutarate and dioxygen genomic region showed consistent linkage. This genetic as cosubstrates, reverse alkylated DNA and RNA damages interval encompasses 28 genes that were all systematically 1INSERM U781 and De´partement de Ge´ne´tique, Universite´ Paris Descartes, Hoˆpital Necker-Enfants Malades, 75015 Paris, France; 2Department of Medical Genetics, Assaf Harofeh, Medical Center, Zerifin, The Sackler School of Medicine, Tel Aviv University, Tel Aviv 70300, Israel; 3Institute of Metabolic Science, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK; 4Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, Hertfordshire EN6 3LD, UK; 5CNRS 8090-Institute of Biology, Pasteur Institute, 59019 Lille, France; 6Section of Genomic Medicine, Ham- mersmith Hospital, Imperial College London, London W12 0NN, UK 7These authors contributed equally to this work *Correspondence: [email protected] DOI 10.1016/j.ajhg.2009.06.002. ª2009 by The American Society of Human Genetics. All rights reserved. 106 The American Journal of Human Genetics 85, 106–111, July 10, 2009 AB C Figure 1. Genetic Analysis of a Family with Ante- and Postnatal Growth Retardation and a Severe Polymalformative Syndrome (A) Pedigree of the family. Filled symbols and slashes indicate affected and deceased infants. (B) Electrophoregrams showing the variation of FTO gene sequence in an affected infant and a healthy control. (C) Part of the multiple sequence alignment of FTO representative orthologs (H.s, Homo sapiens; Ma.m, Macaca mulatta; R.n, Rattus nor- vegicus; Mu.m, Mus musculus; C.f, Canis familiaris; E.c, Equus caballus; Or.a, Ornithorhynchus anatinus; Ov.a, Ovis aries; B.t, Bos taurus; M.d, Monodelphis domestica; G.g, Gallus gallus; D.r, Danio rerio; X.t, Xenopus tropicalis; ABH2 H.s, human ABH2; ABH3 H.s, Human ABH3; AlkB E.c, E. coli AlkB). The conserved residues are highlighted and the amino acid highlighted in red is the absolutely conserved arginine involved in the R316Q mutation in patients (Ai, affected infant). Blue strands labeled with roman numerals identify three of the eight b strands that form the conserved double-stranded b-helix of the 2OG-oxygenases. analyzed at both DNA and/or RNA levels (Table S1). We dren with partially overlapping clinical features were tested identified a homozygous single-nucleotide variation at but no mutation in the FTO gene was identified, strength- cDNA position 947 (c.947G/A) within the FTO gene ening the idea that the new syndrome described here is (Figure 1B). The c.947G/A transition predicts a p.R316Q a very rare condition. substitution. Notably, this amino acid residue is absolutely FTO belongs to the AlkB-related protein family and was conserved across all known FTO paralogs and AlkB ortho- shown to localize in the nucleus.9 Immunofluorescence logs (Figure 1C) and is involved in 2-oxoglutarate coordina- experiments performed on patient and control fibroblasts tion by forming stabilizing salt bridges with the carboxyl- demonstrated that the mutation did not affect its nuclear ates of this cosubstrate.9 This variant cosegregated with localization (data not shown). Murine and human Fto the disease and was not found in 730 control chromosomes, have been shown to demethylate 3-methylthymine and including 378 chromosomes from individuals of Palesti- 3-methyluracil residues in single-stranded DNA and RNA nian Arab origin. We subsequently undertook to estimate in vitro, albeit with a relatively low efficiency. Fto was less the frequency of FTO sequence variants within the general active on the more common forms of methylated DNA base population. FTO coding exons and intron-exon boundaries damage, 1-methyladenine and 3-methylcytosine.9–14,16 sequence was determined in 1492 controls of European Moreover, the recombinant